Enrichment and visualization of small replication units from cultured mammalian cells

Ori-somes, nucleoprotein complexes descending from origin regions of animal chromosomal DNA replication. A micromorphological study

Micromorphology of nucleoprotein (NP) complexes designated according to their descent and shape as Ori-somes is presented. These NP complexes of three different types harbor molecules of cytoplasmic "small" polydisperse DNA, which descend from origin regions of chromosomal DNA replication and are equipped, as shown previously, with early DNA-synthesizing activities. By negative staining the Ori-somes are visualized as particles of irregular shape, sometimes of a subunit-like structure. Micromorphological differences in size and structural compactness noted among individual Ori-somes are dependent on their type similarly as earlier shown physico-chemically and biochemically. Such differences were also confirmed by two different spreading techniques. The most unravelled structures with electron diffuse centers belong to Ori-somes of component B associated with most active DNA synthesis. In contrast, the Ori-somes of components A and C, associated with pronounced RNA synthesis, revealed large electron-dense centers. The incidence of replicative structures present in Ori-somes corresponds with the level of their DNA-synthesizing activities.

DNA changes involved in the formation of metaphase chromosomes, as observed in mouse duodenal crypt cells stained by osmium-ammine. II. Tracing nascent DNA by bromodeoxyuridine into structures arising during the S phase

BACKGROUND

Since it has been found that new chromatin structures make their appearance in the nucleus during the DNA-synthesizing or S phase of the cell cycle, the question arises as to how these structures are related to the nascent DNA.

METHODS

DNA-containing structures were detected in sections of mouse duodenal crypt cells by the DNA-specific osmium-ammine procedure. In the same sections, the nascent or newly-replicated DNA was localized during stages I-IV of the cell cycle (corresponding to four successive parts of the S phase) by immunogold labeling of the DNA precursor bromodeoxyuridine (BrdU) in mice sacrificed 10 min after its injection. Moreover, the fate of the nascent DNA with time was traced up to 6 hr after the injection. (The nomenclature of the DNA-containing structures is that proposed by El-Alfy et al., 1995.)

RESULTS

Ten minutes after BrdU injection, the gold particles indicative of nascent DNA are associated with discrete nucleofilaments scattered in the nucleoplasm, but not with the compacted nucleofilaments making up the heterochromatin or the new S phase structures named "aggregates." The gold-particle-associated discrete nucleofilaments are classified into three types: a) The "free" nucleofilaments have been given this name, since they appear to be independent of heterochromatin and aggregates; nearly all gold particles are over these at stage I; but the numbers of particles over them decreases from stage I to IV. b) The "aggregate-attached" nucleofilaments project from the surface of the aggregates; the number of particles over these is high at stages II and III but decreases at stage IV. c) The "heterochromatin-attached" nucleofilaments project from the surface of the heterochromatin; the number of particles over these increases from stage II to IV. By 1 hr after BrdU injection, gold particles can be over loose clumps of nucleofilaments at stages I and II, but are mostly over small aggregates at stage II, midsized aggregates and small heterochromatin-associated "bulges" at stage III and large aggregates and large bulges at stage IV. By 2-6 hr, virtually all particles are over aggregates and bulges, frequently deep within them.

CONCLUSIONS

The distribution of the gold particles at 10 min reveals that DNA is synthesized in discrete nucleofilaments that are "free" or "aggregate-attached" or "heterochromatin-attached." In contrast, by one and especially two hours, the gold particles are present over aggregates and bulges, indicating that, after discrete nucleofilaments acquire nascent DNA, they are displaced to become part of these structures. More precisely, the aggregates arise from the repeated addition of replicated portions of "free" nucleofilaments, while the bulges arise from the repeated addition of replicated portions, of "heterochromatin-attached" nucleofilaments. Aggregates and bulges are the two initial building stones from which mitotic chromosomes are eventually formed.

Replication forks are underrepresented in chromosomal DNA of Xenopus laevis embryos

Chromosomal DNA was isolated from rapidly dividing cells of Xenopus laevis embryos at blastulation, at gastrulation, and at the beginning of hatching. Few, if any, replication forks were seen by electron microscopy in DNA isolated at any stage of embryogenesis. Instead, unbranched DNA, which appeared to be single-stranded, was abundant at all stages. The percentage of chromosomal DNA that was single-stranded was quantitated by electron microscopy and by monitoring the release of acid-soluble radioactivity during digestion of labeled chromosomal DNA with nucleases specific for single-stranded DNA. The amount of single-stranded DNA was inversely correlated with the length of S phase during embryogenesis. We postulate that chromosomal DNA replication in X. laevis embryos takes place by a mechanism in which strand separation is uncoupled from DNA synthesis.

Replication of mammalian DNA in bromodeoxyuridine: appearance of a component with intermediate density

When three lines of mammalian cells were cultured with 5-bromodeoxyuridine (BrdUrd) for less than one generation, their DNAs displayed three peaks in CsCl gradients. In addition to the expected unsubstituted (LL) and hybrid (LH) peaks, there was a significant absorbance peak of intermediate density (INT) between LH and LL DNAs. This INT DNA has characteristics expected of an intermediate of DNA replication. Upon shearing, it behaves as though it contains contiguous segments of unsubstituted and hybrid DNAs. Upon continuous exposure of cells to [3H]-BrdUrd, radioactivity accumulates in INT DNA for 60-90 min when a steady state condition is reached. At that time, the rate of incorporation into LH DNA increases, consistent with a precursor-product relationship. In a pulse-chase experiment, radioactivity is chased from INT DNA into LH DNA. To account for the above observations and for the size and sharpness of the INT DNA peak in CsCl, we suggest that a high molecular weight replication intermediate accumulates before completing replication into mature daughter molecules.